ephemeris/tests/run_data_managers.yaml.test at master · galaxyproject/ephemeris · GitHub

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# Sample file for testing run-data-managers
genomes:
    - accession: NC_001617.1
      name: RhinoVirus A (NC_001617.1)
      id: RhinoVirusA
    - accession: AC_000007.1
      name: Human adenovirus 2 (AC_000007.1)
      id: HumAdeno2
    - accession: KF039736.1
      name: Norovirus Hu/GI.1/CHA7A011/2010/USA
      id: NoroVirCHA7A011

data_managers:
    - id: data_manager_fetch_genome_all_fasta_dbkey
      params:
        - 'dbkey_source|dbkey_source_selector': 'new'
        - 'dbkey_source|dbkey': '{{ item.id }}'
        - 'dbkey_source|dbkey_name': '{{ item.name }}'
        - 'sequence_name': '{{ item.name }}'
        - 'sequence_id': '{{ item.id }}'
        - 'reference_source|reference_source_selector': 'ncbi'
        - 'reference_source|requested_identifier': '{{ item.accession }}'
      items: "{{ genomes }}"
      data_table_reload:
        - all_fasta
        - __dbkeys__

    - id: sam_fasta_index_builder
      params:
        - 'all_fasta_source': '{{ item.id }}'
        - 'sequence_name': '{{ item.name }}'
        - 'sequence_id': '{{ item.id }}'
      items: "{{ genomes }}"
      data_table_reload:
        - fasta_indexes

    - id: bwa_mem_index_builder_data_manager
      params:
        - 'all_fasta_source': '{{ item.id }}'
        - 'sequence_name': '{{ item.name }}'
        - 'sequence_id': '{{ item.id }}'
      items: "{{ genomes }}"
      data_table_reload:
        - bwa_mem_indexes